Ecosyste.ms: Issues

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GitHub / molgenis/molgenis-pipelines issues and pull requests

#100 - Check comments

Pull Request - State: closed - Opened by kantale almost 11 years ago - 1 comment

#99 - public rna seq

Pull Request - State: closed - Opened by PatrickDeelen almost 11 years ago

#98 - In-house pipeline upto variant calling

Pull Request - State: closed - Opened by freerkvandijk almost 11 years ago

#97 - See comments

Pull Request - State: closed - Opened by kantale almost 11 years ago

#96 - Implemented new protocols in-house NGS pipeline

Pull Request - State: closed - Opened by freerkvandijk almost 11 years ago

#95 - NGS 5 genes per minute pipeline in Compute4.

Pull Request - State: closed - Opened by Gerbenvandervries almost 11 years ago

#94 - Updates in-house NGS alignment pipeline compute5

Pull Request - State: closed - Opened by freerkvandijk about 11 years ago

#93 - Updates and bugfixes Lifelines genotype pipeline

Pull Request - State: closed - Opened by freerkvandijk about 11 years ago

#91 - Lifelines update genotype pipeline

Pull Request - State: closed - Opened by freerkvandijk about 11 years ago

#90 - Fixed bins

Pull Request - State: closed - Opened by PatrickDeelen about 11 years ago

#89 - Output directory for generated FinalReport changed.

Pull Request - State: closed - Opened by Gerbenvandervries about 11 years ago

#88 - Added genotype Aligner step

Pull Request - State: closed - Opened by kantale about 11 years ago - 3 comments

#86 - Fix bug in worksheet test

Pull Request - State: closed - Opened by PatrickDeelen about 11 years ago

#85 - Impute2 small update

Pull Request - State: closed - Opened by PatrickDeelen about 11 years ago

#83 - fix path in worksheet

Pull Request - State: closed - Opened by georgebyelas about 11 years ago

#81 - removed parameter, which can be useful, but now it is blocker

Pull Request - State: closed - Opened by georgebyelas about 11 years ago

#80 - RNA-seq_genotype_calling pipeline compute5 style

Pull Request - State: closed - Opened by freerkvandijk about 11 years ago

#77 - Removed mapping in 2 workflows, and added echo-ing to a protocol.

Pull Request - State: closed - Opened by Gerbenvandervries over 11 years ago

#76 - Bcl2FastQ and Createruns pipelines for Compute5

Pull Request - State: closed - Opened by Gerbenvandervries over 11 years ago

#75 - Fixed some bugs in RNA-seq_quantify_gene_level pipeline

Pull Request - State: closed - Opened by DashaZhernakova over 11 years ago

#74 - Bugfix haloplex pipeline + compute5 in-house

Pull Request - State: closed - Opened by freerkvandijk over 11 years ago

#72 - RNA-seq pipelines updates

Pull Request - State: closed - Opened by PatrickDeelen over 11 years ago

#71 - Updates on bcl2fastq pipeline

Pull Request - State: closed - Opened by freerkvandijk over 11 years ago

#70 - Final edits in order to fix dependencies in impute2 pipeline for compute5

Pull Request - State: closed - Opened by kantale over 11 years ago

#69 - Fix of an error in shapeit. By mistake i deleted part of the protocol..

Pull Request - State: closed - Opened by kantale over 11 years ago

#67 - Updates to diverse pipelines

Pull Request - State: closed - Opened by PatrickDeelen over 11 years ago

#66 - corrected a foreach remnant in a compute 5 protocol

Pull Request - State: closed - Opened by kantale over 11 years ago

#65 - Bug fixes in SNVMix to gen converter

Pull Request - State: closed - Opened by DashaZhernakova over 11 years ago

#64 - RNA-seq pipelines updates

Pull Request - State: closed - Opened by PatrickDeelen over 11 years ago

#63 - SNVMix to gen converter added

Pull Request - State: closed - Opened by DashaZhernakova over 11 years ago

#62 - Updates on Haloplex pipeline

Pull Request - State: closed - Opened by freerkvandijk over 11 years ago

#61 - RNA-seq pipelines udates

Pull Request - State: closed - Opened by PatrickDeelen over 11 years ago

#60 - Bugfixes in haloplex pipeline

Pull Request - State: closed - Opened by freerkvandijk over 11 years ago

#59 - RNA-seq pipelines udates

Pull Request - State: closed - Opened by PatrickDeelen over 11 years ago

#58 - Added RNA-seq genotype calling pipeline

Pull Request - State: closed - Opened by DashaZhernakova over 11 years ago

#57 - Imputation_shapeit_phasing misses readme.md

Issue - State: open - Opened by PatrickDeelen over 11 years ago
Labels: bug

#56 - update star aligner

Pull Request - State: closed - Opened by PatrickDeelen over 11 years ago

#55 - Added RNA-seq STAR alignment pipeline

Pull Request - State: closed - Opened by DashaZhernakova over 11 years ago

#54 - Added impute2 pipeline for compute5

Pull Request - State: closed - Opened by kantale over 11 years ago

#53 - Several fixes in HaloPlex pipeline

Pull Request - State: closed - Opened by freerkvandijk over 11 years ago

#52 - Small fix in CopyToResultDir

Pull Request - State: closed - Opened by freerkvandijk over 11 years ago

#51 - First version Haloplex pipeline + bugfix in-house pipeline

Pull Request - State: closed - Opened by freerkvandijk over 11 years ago

#49 - added 2 <noparse> tags in BCLtoFqBcl2FastQ.ftl

Pull Request - State: closed - Opened by Gerbenvandervries over 11 years ago

#48 - Changed path to getStatisticsScript in parameter file

Pull Request - State: closed - Opened by Gerbenvandervries over 11 years ago

#47 - Changed mismatches per lane, to max(0 or 1) mismatches per run

Pull Request - State: closed - Opened by Gerbenvandervries over 11 years ago

#46 - Added CreateCoverageBedFile protocol

Pull Request - State: closed - Opened by freerkvandijk over 11 years ago

#45 - Changed getstatisticsscriptpath to newest location

Pull Request - State: closed - Opened by ljohansson over 11 years ago

#44 - Change in CreateInhouseProjects.ftl

Pull Request - State: closed - Opened by Gerbenvandervries over 11 years ago

#43 - changed location of workflowFile in in-house_parameters_gpfs.csv

Pull Request - State: closed - Opened by ljohansson over 11 years ago

#41 - Quick concordance check pipeline

Pull Request - State: closed - Opened by freerkvandijk over 11 years ago

#39 - Update on mergeIndelCalls protocol

Pull Request - State: closed - Opened by freerkvandijk over 11 years ago

#38 - Added dataTransfer protocol

Pull Request - State: closed - Opened by freerkvandijk over 11 years ago

#37 - Improved demultiplex protocol

Pull Request - State: closed - Opened by pneerincx over 11 years ago

#36 - Small fixes for the data archiving workflow.

Pull Request - State: closed - Opened by pneerincx over 11 years ago

#35 - Small fixes for the GAF data archiving workflow.

Pull Request - State: closed - Opened by pneerincx over 11 years ago

#34 - Fixed bugs in GAF/Bcl2Fastq workflow.

Pull Request - State: closed - Opened by pneerincx over 11 years ago

#33 - Added parameter for the latest dbSNP version.

Pull Request - State: closed - Opened by pneerincx over 11 years ago

#32 - Bugfix VCF to Table protocol

Pull Request - State: closed - Opened by freerkvandijk over 11 years ago - 1 comment

#31 - Updated GAF workflow to create array final reports per sample.

Pull Request - State: closed - Opened by pneerincx over 11 years ago

#30 - NGS_de_novo_assembly workflow improvements

Pull Request - State: closed - Opened by pneerincx over 11 years ago

#29 - Updated walltimes in impute2 pipeline

Pull Request - State: closed - Opened by freerkvandijk over 11 years ago

#28 - added templates parameter to CreateInHouseProjects.ftl

Pull Request - State: closed - Opened by ljohansson over 11 years ago

#27 - Added protocol to merge PED/MAP files

Pull Request - State: closed - Opened by kantale over 11 years ago

#25 - changes in GWAS and Imputation_minimac pipelines

Pull Request - State: closed - Opened by kantale over 11 years ago

#24 - Added concordance protocol for Imputation_minimac

Pull Request - State: closed - Opened by kantale over 11 years ago - 1 comment

#23 - Fixed all outputs exists in impute2 pipeline

Pull Request - State: closed - Opened by PatrickDeelen over 11 years ago

#22 - Small updates on impute2 pipeline

Pull Request - State: closed - Opened by freerkvandijk over 11 years ago

#21 - Production ready shapeit2 and liftover pipeline

Pull Request - State: closed - Opened by freerkvandijk over 11 years ago

#20 - ShapeIt2 pipeline

Pull Request - State: closed - Opened by PatrickDeelen over 11 years ago

#19 - Production ready studyQC pipeline

Pull Request - State: closed - Opened by freerkvandijk over 11 years ago

#18 - First version of imputation study QC pipeline

Pull Request - State: closed - Opened by freerkvandijk over 11 years ago

#17 - Bug fix in parameters

Pull Request - State: closed - Opened by georgebyelas over 11 years ago

#16 - Impute2 update and readme update

Pull Request - State: closed - Opened by PatrickDeelen over 11 years ago

#15 - Impute2 updates

Pull Request - State: closed - Opened by PatrickDeelen over 11 years ago

#14 - test worksheet impute2

Pull Request - State: closed - Opened by PatrickDeelen over 11 years ago

#12 - Bugfix in impute2Imputation.ftl

Pull Request - State: closed - Opened by freerkvandijk over 11 years ago

#11 - Bugfix in impute2 protocol

Pull Request - State: closed - Opened by freerkvandijk over 11 years ago

#10 - Added new GAF and de-novo assembly workflows + updated gitignore.

Pull Request - State: closed - Opened by pneerincx over 11 years ago

#9 - Added new GAF and de-novo assembly workflows + updated gitignore.

Pull Request - State: closed - Opened by pneerincx over 11 years ago

#8 - Impute2 merge ref small updates

Pull Request - State: closed - Opened by PatrickDeelen over 11 years ago

#7 - Small merge ref impute2 update

Pull Request - State: closed - Opened by PatrickDeelen over 11 years ago

#6 - Added Data Archiving pipeline

Pull Request - State: closed - Opened by ljohansson over 11 years ago

#5 - added missing templates

Pull Request - State: closed - Opened by georgebyelas over 11 years ago

#4 - Removed redundant folders

Pull Request - State: closed - Opened by mdijkstra over 11 years ago

#3 - Impute 2 updates

Pull Request - State: closed - Opened by PatrickDeelen over 11 years ago

#2 - started new workflow repository structure

Pull Request - State: closed - Opened by georgebyelas over 11 years ago